# # ChangeLog for src/FunctionApproximation # # Generated by Trac 1.4.4 # Dec 28, 2024, 12:07:48 PM Thu, 02 Mar 2017 07:14:22 GMT Frederik Heber [4ecb2d] * LinearAlgebra/doc/am_doxygen_include.am (deleted) * LinearAlgebra/m4 (deleted) * Makefile.am (modified) * ThirdParty/LinearAlgebra/.gitignore (moved) * ThirdParty/LinearAlgebra/AUTHORS (moved) * ThirdParty/LinearAlgebra/COPYING (moved) * ThirdParty/LinearAlgebra/ChangeLog (moved) * ThirdParty/LinearAlgebra/INSTALL (moved) * ThirdParty/LinearAlgebra/LinearAlgebra-debug.pc.in (moved) * ThirdParty/LinearAlgebra/LinearAlgebra.pc.in (moved) * ThirdParty/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/NEWS (moved) * ThirdParty/LinearAlgebra/README (moved) * ThirdParty/LinearAlgebra/bootstrap (moved) * ThirdParty/LinearAlgebra/build-aux/README (moved) * ThirdParty/LinearAlgebra/configure.ac (moved) * ThirdParty/LinearAlgebra/doc/Doxyfile (moved) * ThirdParty/LinearAlgebra/doc/Makefile.am (moved) * ThirdParty/LinearAlgebra/doc/am_doxygen_include.am (added) * ThirdParty/LinearAlgebra/libLinearAlgebra_config.h.in (moved) * ThirdParty/LinearAlgebra/m4 (added) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/BoxVector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Exceptions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Line.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinePoint.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegment.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LineSegmentSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/LinearSystemOfEquations.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/MatrixVector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Plane.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/RealSpaceMatrix.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Space.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/Vector.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorContent.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorInterface.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/VectorSet.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/defs.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/fast_functions.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/leastsquaremin.hpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.cpp (moved) * ThirdParty/LinearAlgebra/src/LinearAlgebra/vector_ops.hpp (moved) * ThirdParty/LinearAlgebra/src/documentation/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/documentation/groups.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/lines.dox (moved) * ThirdParty/LinearAlgebra/src/documentation/mainpage.dox (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LineUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/LinearSystemOfEquationsUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/Makefile.am (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentSymmetricUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/MatrixContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/PlaneUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/RealSpaceMatrixUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/TestRunnerMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/UnitTestMain.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorContentUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorSetUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.cpp (moved) * ThirdParty/LinearAlgebra/src/unittests/VectorUnitTest.hpp (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/Makefile.am (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/atlocal.in (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-config_h.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-date_in_dox.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-header-dist.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-memdebug.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite-project-disclaimer.at (moved) * ThirdParty/LinearAlgebra/tests/CodeChecks/testsuite.at (moved) * configure.ac (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) Moved LinearAlgebra sub-package into ThirdParty folder. - needed to ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [1155ba] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Converted filterArguments... into faster filter, renamed other to ... Fri, 11 Nov 2016 14:25:36 GMT Frederik Heber [9c793c] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Improper.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) All ..Potentials now return BindingModel instead of HomologyGraph, ... Fri, 11 Nov 2016 14:25:30 GMT Frederik Heber [2124aa] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) Extractors::reorderArgumentsByParticleTypes() rewritten to scan for ... Fri, 04 Nov 2016 11:47:34 GMT Frederik Heber [228340] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) Extractors::gatherAllSymmetricDistances..() additionaly gets edge set ... Fri, 04 Nov 2016 09:37:52 GMT Frederik Heber [2ae400] * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) Added bonded flag to argument_t. Fri, 04 Nov 2016 09:37:51 GMT Frederik Heber [e60558] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) Extractors require additionally the binding graph of the fragment ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [67044a] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) Extractors require additional binding model which EmpiricalPotentials ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [c5e75f3] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/SerializablePotential.hpp (modified) * src/documentation/constructs/potentials.dox (modified) ParticleType_t is now an unsigned int. - this allows direct use of ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [c7aac9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) FIX: TrainingData used charges instead of atomic numbers to recognize ... Fri, 04 Nov 2016 09:37:50 GMT Frederik Heber [e47ac7] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) REFACTOR: Removed many unused functions from Extractor namespace. - ... Tue, 09 Feb 2016 07:11:35 GMT Frederik Heber [b40690] * doc/userguide/userguide.xml (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitCompoundPotentialAction.def (modified) * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/Actions/PotentialAction/FitPotentialAction.def (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * src/Potentials/PotentialTrainer.hpp (modified) * tests/Python/AllActions/options.dat (modified) Fit..PotentialAction now allow setting maximum number of optimization ... Tue, 09 Feb 2016 07:10:23 GMT Frederik Heber [b8f2ea] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/PotentialTrainer.cpp (modified) * tests/regression/Potential/FitPotential/testsuite-potential-fit-potential.at (modified) FIX: PotentialTrainer did not use user-specified threshold so far. ... Thu, 21 Aug 2014 06:43:46 GMT Frederik Heber [748fc7] * src/Actions/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/builder_init.cpp (modified) * src/unittests/Makefile.am (modified) libMolecuilder is now a shared library. - linking error ... Wed, 20 Aug 2014 12:59:14 GMT Frederik Heber [e9e86f] * src/Actions/unittests/Makefile.am (modified) * src/Analysis/unittests/Makefile.am (modified) * src/Atom/unittests/Makefile.am (modified) * src/Descriptors/unittests/Makefile.am (modified) * src/Element/unittests/Makefile.am (modified) * src/Filling/unittests/Makefile.am (modified) * src/Fragmentation/Exporters/unittests/Makefile.am (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (modified) * src/Fragmentation/Summation/unittests/Makefile.am (modified) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/unittests/Makefile.am (modified) * src/Graph/unittests/Makefile.am (modified) * src/Jobs/unittests/Makefile.am (modified) * src/LinkedCell/unittests/Makefile.am (modified) * src/Parameters/unittests/Makefile.am (modified) * src/Parser/Parameters/unittests/Makefile.am (modified) * src/Parser/unittests/Makefile.am (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) * src/RandomNumbers/unittests/Makefile.am (modified) * src/Shapes/unittests/Makefile.am (modified) * src/Tesselation/unittests/Makefile.am (modified) * src/UIElements/CommandLineUI/unittests/Makefile.am (modified) * src/UIElements/Menu/unittests/Makefile.am (modified) * src/unittests/Makefile.am (modified) * tests/JobMarket/Makefile.am (modified) FIX: UnitTestMain placed into convenience libUnitTest. - removed ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [e1fe7e] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_ImproperUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/FourBodyPotential_TorsionUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_HarmonicUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_LennardJonesUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_MorseUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ThreeBodyPotential_AngleUnitTest.cpp (modified) * src/Potentials/helpers.hpp (modified) * src/Potentials/unittests/CompoundPotentialUnitTest.cpp (modified) * src/UIElements/Views/Qt4/QtHomologyList.cpp (modified) FunctionModel now uses list_of_arguments to split sequence of subsets ... Fri, 27 Jun 2014 21:32:55 GMT Frederik Heber [16227a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.cpp (modified) * src/Potentials/Specifics/PairPotential_LennardJones.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) * src/Potentials/unittests/Makefile.am (modified) Removed FunctionModel::getSpecificExtractor() that is not needed ... Fri, 27 Jun 2014 21:32:29 GMT Frederik Heber [f4496d] * src/Actions/PotentialAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) Extracted associating each configuration with its L2 error into ... Fri, 27 Jun 2014 21:32:29 GMT Frederik Heber [1ba8a1] * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/documentation/constructs/potentials.dox (modified) DOCU: Extended documentation on FunctionApproximation and potential ... Tue, 29 Apr 2014 12:42:43 GMT Frederik Heber [a2a2f7] * src/Actions/ActionSequence.cpp (modified) * src/Actions/SelectionAction/Atoms/AtomByIdAction.cpp (modified) * src/Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp (modified) * src/Actions/ShapeAction/RemoveShapeAction.cpp (modified) * src/Actions/ShapeAction/StretchShapeAction.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Box.cpp (modified) * src/Filling/Mesh/CubeMesh.cpp (modified) * src/Fragmentation/AdaptivityMap.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/FragmentEdge.cpp (modified) * src/Fragmentation/Homology/FragmentNode.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.hpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.hpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/EigenvaluesUnitTest.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/Parameters/Validators/Specific/TimeStepPresentValidator.cpp (modified) * src/Potentials/Specifics/FourBodyPotential_Torsion.cpp (modified) * src/Potentials/Specifics/ThreeBodyPotential_Angle.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/Tesselation/tesselation.cpp (modified) * src/Tesselation/tesselationhelpers.cpp (modified) * src/UIElements/Qt4/Query/QtQueryList.hpp (modified) * src/UIElements/Qt4/Query/VectorQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Plotting/QSeisPlotPage.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/QtTimeLine.cpp (modified) Huge warning fix. - fixed unused variables. - fixed set but unused ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [bf1d1b] * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.def (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.cpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/HomologyContainerUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * tests/Python/AllActions/options.dat (modified) HomologyContainer now stores full struct as value to HomologyGraph ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [af2c7ec] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) TrainingData now generates internal list of all arguments. - ... Fri, 09 Aug 2013 14:20:36 GMT Frederik Heber [31a2be] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractors::filterArgumentsByParticleTypes() did wrongly break ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [51e0e3] * configure.ac (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) Added two filter functions to Extractors. - renamed ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [0f5d38] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/helpers.hpp (modified) Added getSpecificFilter() and getSpecificArgumentCount() to ... Fri, 09 Aug 2013 14:20:35 GMT Frederik Heber [f0025d] * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/CompoundPotential.cpp (modified) * src/Potentials/CompoundPotential.hpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (modified) * src/Potentials/Specifics/ConstantPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Renamed getFragmentSpecificExtractor() -> getSpecificExtractor(). Mon, 08 Jul 2013 14:22:02 GMT Frederik Heber [cf4905] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added concatenateArguments to Extractors. Mon, 08 Jul 2013 14:22:01 GMT Frederik Heber [8203ce8] * src/FunctionApproximation/Extractors.cpp (modified) * src/Potentials/Makefile.am (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/Specifics/ConstantPotential.cpp (added) * src/Potentials/Specifics/ConstantPotential.hpp (added) * src/Potentials/Specifics/PotentialTypes.def (modified) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.cpp (added) * src/Potentials/Specifics/unittests/ConstantPotentialUnitTest.hpp (added) * src/Potentials/Specifics/unittests/Makefile.am (modified) Added ConstantPotential to fit a non-zero offset in potential energy. ... Mon, 08 Jul 2013 14:22:00 GMT Frederik Heber [bb1f3f] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Removed doubly present inclusions from Extractors. - these are ... Wed, 12 Jun 2013 10:11:59 GMT Frederik Heber [5aaa43] * src/Actions/ActionRegistry.cpp (modified) * src/Actions/FragmentationAction/AnalyseFragmentationResultsAction.cpp (modified) * src/Actions/FragmentationAction/FitPotentialAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAction.cpp (modified) * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Actions/FragmentationAction/ParseFragmentJobsAction.cpp (modified) * src/Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp (modified) * src/Actions/GraphAction/CreateAdjacencyAction.cpp (modified) * src/Actions/GraphAction/DestroyAdjacencyAction.cpp (modified) * src/Actions/GraphAction/SubgraphDissectionAction.cpp (modified) * src/Actions/GraphAction/UpdateMoleculesAction.cpp (modified) * src/Actions/MakroAction.cpp (modified) * src/Actions/SelectionAction/Atoms/AllAtomsInsideVolumeAction.cpp (modified) * src/Actions/WorldAction/RepeatBoxAction.cpp (modified) * src/Actions/unittests/ActionSequenceUnitTest.cpp (modified) * src/Analysis/analysis_correlation.cpp (modified) * src/Analysis/unittests/AnalysisPairCorrelationUnitTest.cpp (modified) * src/Atom/AtomObserver.cpp (modified) * src/Atom/CopyAtoms/CopyAtoms_withBonds.cpp (modified) * src/Atom/atom.cpp (modified) * src/Atom/atom_bondedparticle.cpp (modified) * src/Atom/atom_observable.cpp (modified) * src/Atom/unittests/AtomObserverUnitTest.cpp (modified) * src/Bond/BondInfo.cpp (modified) * src/Bond/bond.cpp (modified) * src/Bond/bond_observable.cpp (modified) * src/Box.cpp (modified) * src/Descriptors/unittests/AtomDescriptorUnitTest.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.cpp (modified) * src/Fragmentation/Automation/VMGFragmentController.cpp (modified) * src/Fragmentation/BondsPerShortestPath.cpp (modified) * src/Fragmentation/Exporters/ExportGraph.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToFiles.cpp (modified) * src/Fragmentation/Exporters/ExportGraph_ToJobs.cpp (modified) * src/Fragmentation/Exporters/HydrogenPool.cpp (modified) * src/Fragmentation/Exporters/SaturatedFragment.cpp (modified) * src/Fragmentation/Exporters/unittests/HydrogenPoolUnitTest.cpp (modified) * src/Fragmentation/Exporters/unittests/SaturatedFragmentUnitTest.cpp (modified) * src/Fragmentation/ForceMatrix.cpp (modified) * src/Fragmentation/Fragmentation.cpp (modified) * src/Fragmentation/Homology/HomologyGraph.cpp (modified) * src/Fragmentation/Homology/unittests/HomologyGraphUnitTest.cpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/KeySetsContainer.cpp (modified) * src/Fragmentation/PowerSetGenerator.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationResultContainer.cpp (modified) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (modified) * src/Fragmentation/Summation/Containers/MPQCData.cpp (modified) * src/Fragmentation/Summation/Containers/VMGData.cpp (modified) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (modified) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (modified) * src/Fragmentation/Summation/IndexSetContainer.cpp (modified) * src/Fragmentation/Summation/SetValues/Eigenvalues.cpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (modified) * src/Fragmentation/Summation/SetValues/Histogram.cpp (modified) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (modified) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (modified) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (modified) * src/Fragmentation/Summation/SubsetMap.cpp (modified) * src/Fragmentation/fragmentation_helpers.cpp (modified) * src/Fragmentation/parseKeySetFile.cpp (modified) * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Graph/BondGraph.cpp (modified) * src/Graph/BuildInducedSubgraph.cpp (modified) * src/Graph/DepthFirstSearchAnalysis.cpp (modified) * src/Graph/unittests/AdjacencyListUnitTest.cpp (modified) * src/Jobs/InterfaceVMGJob.cpp (modified) * src/Jobs/MPQCJob.cpp (modified) * src/Jobs/VMGJob.cpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LinkedCell/LinkedCell_Controller.cpp (modified) * src/LinkedCell/unittests/stubs/AtomObserverStub.cpp (modified) * src/LinkedCell/unittests/stubs/ObserverBoxStub.cpp (modified) * src/LinkedCell/unittests/stubs/WorldTimeStub.cpp (modified) * src/Parameters/Validators/Specific/PotentialTypeValidator.cpp (modified) * src/Parser/MpqcParser.cpp (modified) * src/Parser/PcpParser.cpp (modified) * src/Parser/PcpParser_helper.cpp (modified) * src/Parser/PdbParser.cpp (modified) * src/Parser/Psi3Parser.cpp (modified) * src/Parser/TremoloParser.cpp (modified) * src/Parser/XmlParser.cpp (modified) * src/Parser/XyzParser.cpp (modified) * src/Parser/unittests/ParserMpqcUnitTest.cpp (modified) * src/Parser/unittests/ParserPcpUnitTest.cpp (modified) * src/Parser/unittests/ParserPdbUnitTest.cpp (modified) * src/Parser/unittests/ParserPsi3UnitTest.cpp (modified) * src/Parser/unittests/ParserTremoloUnitTest.cpp (modified) * src/Parser/unittests/ParserXmlUnitTest.cpp (modified) * src/Parser/unittests/ParserXyzUnitTest.cpp (modified) * src/Shapes/BaseShapes.cpp (modified) * src/Shapes/ShapeOps.cpp (modified) * src/Shapes/ShapeRegistry.cpp (modified) * src/Tesselation/CandidateForTesselation.cpp (modified) * src/Tesselation/boundary.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/AtomsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/BooleanCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoubleCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/DoublesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/ElementsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FileCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/FilesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/IntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculeCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/MoleculesCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RandomNumberDistribution_ParametersCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/RealSpaceMatrixCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/StringsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/UnsignedIntsCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorCommandLineQuery.cpp (modified) * src/UIElements/CommandLineUI/Query/VectorsCommandLineQuery.cpp (modified) * src/UIElements/Qt4/QtMainWindow.cpp (modified) * src/UIElements/Qt4/Query/FileQtQuery.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_atom.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_bond.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_molecule.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLMoleculeObject_shape.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldScene.cpp (modified) * src/UIElements/Views/Qt4/Qt3D/GLWorldView.cpp (modified) * src/World.cpp (modified) * src/WorldTime.cpp (modified) * src/cleanUp.cpp (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/molecule.cpp (modified) * src/molecule_graph.cpp (modified) * src/unittests/stubs/WorldStub.cpp (modified) * tests/CodeChecks/testsuite-project-disclaimer.at (modified) * tests/regression/Fragmentation/AnalyseFragmentationResults/testsuite-fragmentation-analyse-fragment-results.at (modified) * tests/regression/Fragmentation/FitPotential/testsuite-fragmentation-fit-potential.at (modified) * tests/regression/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at (modified) * tests/regression/Fragmentation/testsuite-fragmentation.at (modified) * tests/regression/Graph/CreateAdjacency/testsuite-graph-create-adjacency.at (modified) * tests/regression/Graph/DestroyAdjacency/testsuite-graph-destroy-adjacency.at (modified) * tests/regression/Graph/testsuite-graph.at (modified) * tests/regression/Parser/Mpqc/testsuite-parser-mpqc-load.at (modified) * tests/regression/Parser/Xyz/testsuite-parser-xyz-save.at (modified) * tests/regression/testsuite.at (modified) FIX: Fixed new copyright line since start of 2013 in CodeChecks test. ... Fri, 03 May 2013 09:46:46 GMT Frederik Heber [57f14c] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractors::_detail::convertElementcountsToTargets() complains ... Tue, 16 Apr 2013 06:30:39 GMT Frederik Heber [214240] * src/Actions/Makefile.am (modified) * src/Analysis/Makefile.am (modified) * src/Atom/Makefile.am (modified) * src/Element/Makefile.am (modified) * src/Filling/Makefile.am (modified) * src/Fragmentation/Automation/Makefile.am (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/Summation/Containers/Makefile.am (modified) * src/Fragmentation/Summation/Converter/Makefile.am (modified) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/SetValues/Makefile.am (modified) * src/FunctionApproximation/Makefile.am (modified) * src/Graph/Makefile.am (modified) * src/Helpers/Makefile.am (modified) * src/LinkedCell/Makefile.am (modified) * src/Parameters/Makefile.am (modified) * src/Parser/Makefile.am (modified) * src/Potentials/Makefile.am (modified) * src/RandomNumbers/Makefile.am (modified) * src/Shapes/Makefile.am (modified) * src/UIElements/Makefile.am (modified) FIX: Most of the includedirs were wrongly set. - each just needs to ... Mon, 15 Apr 2013 18:13:22 GMT Frederik Heber [fbf143] * src/Actions/FragmentationAction/FragmentationAutomationAction.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.cpp (modified) * src/Fragmentation/Automation/FragmentJobQueue.hpp (modified) * src/Fragmentation/Automation/MPQCFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGDebugGridFragmentController.hpp (modified) * src/Fragmentation/Automation/VMGFragmentController.hpp (modified) * src/Fragmentation/Homology/HomologyContainer.hpp (modified) * src/Fragmentation/Homology/unittests/stubs/FragmentStub.cpp (modified) * src/Fragmentation/Makefile.am (modified) * src/Fragmentation/SetValues/unittests/Makefile.am (deleted) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationChargeDensity.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationLongRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.cpp (moved) * src/Fragmentation/Summation/Containers/FragmentationShortRangeResults.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.cpp (moved) * src/Fragmentation/Summation/Containers/MPQCData.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/MPQCData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/Makefile.am (moved) * src/Fragmentation/Summation/Containers/VMGData.cpp (moved) * src/Fragmentation/Summation/Containers/VMGData.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataFused.hpp (moved) * src/Fragmentation/Summation/Containers/VMGDataMap.hpp (moved) * src/Fragmentation/Summation/Containers/VMGData_printKeyNames.hpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.cpp (moved) * src/Fragmentation/Summation/Containers/createMatrixNrLookup.hpp (moved) * src/Fragmentation/Summation/Containers/extractJobIds.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.cpp (moved) * src/Fragmentation/Summation/Containers/unittests/MPQCDataUnitTest.hpp (moved) * src/Fragmentation/Summation/Containers/unittests/Makefile.am (moved) * src/Fragmentation/Summation/Converter/DataConverter.hpp (moved) * src/Fragmentation/Summation/Converter/Makefile.am (moved) * src/Fragmentation/Summation/Makefile.am (modified) * src/Fragmentation/Summation/OrthogonalSumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/OrthogonalSummator.hpp (modified) * src/Fragmentation/Summation/SetValues/Fragment.cpp (moved) * src/Fragmentation/Summation/SetValues/Fragment.hpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.cpp (moved) * src/Fragmentation/Summation/SetValues/Histogram.hpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.cpp (moved) * src/Fragmentation/Summation/SetValues/IndexedVectors.hpp (moved) * src/Fragmentation/Summation/SetValues/Makefile.am (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.cpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGridProperties.hpp (moved) * src/Fragmentation/Summation/SetValues/SamplingGrid_inline.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/FragmentUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/HistogramUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/IndexedVectorsUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/Makefile.am (added) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridPropertiesUnitTest.hpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.cpp (moved) * src/Fragmentation/Summation/SetValues/unittests/SamplingGridUnitTest.hpp (moved) * src/Fragmentation/Summation/SumUpPerLevel.hpp (modified) * src/Fragmentation/Summation/Summator.hpp (modified) * src/Fragmentation/parseKeySetFile.cpp (moved) * src/Fragmentation/parseKeySetFile.hpp (moved) * src/Fragmentation/unittests/Makefile.am (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/Jobs/InterfaceVMGDebugGridJob.hpp (modified) * src/Jobs/InterfaceVMGJob.hpp (modified) * src/Jobs/MPQCCommandJob.hpp (modified) * src/Jobs/MPQCJob.hpp (modified) * src/Jobs/Makefile.am (modified) * src/Jobs/VMGDebugGridJob.hpp (modified) * src/Jobs/VMGJob.hpp (modified) * src/Jobs/WindowGrid_converter.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) * src/UIElements/Makefile.am (modified) * src/controller_MPQCCommandJob.cpp (modified) * src/unittests/Makefile.am (modified) Placed Containers, Converter, and SetValues as subfolders into ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [64bdfd] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) Changed Extractor's combineArguments() to neglect same arguments. - ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [035c0d] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/PotentialFactory.cpp (modified) * src/Potentials/PotentialFactory.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) Removed typedef charges_t from FunctionModel, using ... Wed, 27 Feb 2013 12:43:29 GMT Frederik Heber [da2d5c] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) Removed parameter charges from getFragmentSpecificExtractor(). Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [e36ba2] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) FunctionModel extended by triplefunction setter, does nothing by ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [d52819] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) Extracted initial parameter setting per specific potential to ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [7b019a] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Angle.cpp (modified) * src/Potentials/Specifics/PairPotential_Angle.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.cpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) * src/Potentials/Specifics/SaturationPotential.cpp (modified) * src/Potentials/Specifics/SaturationPotential.hpp (modified) * src/Potentials/Specifics/unittests/Makefile.am (modified) Extended FunctionModel by getFragmentSpecificExtractor() definition. ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [69fcba] * src/FunctionApproximation/Extractors.cpp (modified) FIX: Extractor's convertTargetsToArguments() did not set argument_t's ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [9897ee9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added combineArguments to Extractors. - this is required for ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [df350c] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added reorderArgumentsByParticleTypes() to Extractors. - this is ... Wed, 27 Feb 2013 12:39:03 GMT Frederik Heber [caa00e9] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Added gatherAllDistancesFromFragment() to Extractors. - ... Mon, 25 Feb 2013 17:28:58 GMT Frederik Heber [691be4] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/FunctionArgument.cpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/PairPotential_AngleUnitTest.cpp (modified) FunctionArgument now contains charges, too, and rewrote Extractors ... Mon, 25 Feb 2013 17:28:57 GMT Frederik Heber [dd8094] * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/LevMartester.cpp (modified) Added getTrainingOutputAverage() used to initialize all_energy_offset ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [04cc7e] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (modified) * src/FunctionApproximation/TrainingData.hpp (modified) * src/FunctionApproximation/writeDistanceEnergyTable.hpp (added) * src/LevMartester.cpp (modified) Added pretty printer for distance-energy tables. - added ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [52e7da] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (modified) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (modified) * src/LevMartester.cpp (modified) Angle training now also uses TrainingData. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [ac868ee] * src/FunctionApproximation/unittests/ExtractorsUnitTest.cpp (added) * src/FunctionApproximation/unittests/ExtractorsUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (modified) Added unit test for functions in Extractors namespace. Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [49f163] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Added gatherAllSymmetricDistanceArguments(). - using it for ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [63e786] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored realignElementTargets() out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [c211f7] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored convertElementcountsToTargets() out of ... Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [bc6705] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) Refactored getElementCounts out of gatherDistancesOfTuples(). Sun, 24 Feb 2013 12:58:53 GMT Frederik Heber [301dbf] * src/FunctionApproximation/Extractors.cpp (modified) * src/FunctionApproximation/Extractors.hpp (modified) * src/LevMartester.cpp (modified) Refactored gatherDistanceOfTuples(). - it is now able to work on ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [69ab84] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/LevMartester.cpp (modified) FunctionApproximation's cstor now accepts TrainingData instance directly. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [68172a] * src/FunctionApproximation/Makefile.am (modified) * src/FunctionApproximation/TrainingData.cpp (added) * src/FunctionApproximation/TrainingData.hpp (added) * src/LevMartester.cpp (modified) Shifted class TrainingData into its own module. Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [8aa597] * src/FunctionApproximation/Extractors.cpp (added) * src/FunctionApproximation/Extractors.hpp (added) * src/FunctionApproximation/Makefile.am (modified) * src/LevMartester.cpp (modified) Extracted namespace Extractors into own module. - placed ... Sun, 24 Feb 2013 12:58:52 GMT Frederik Heber [355af8] * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.cpp (added) * src/FunctionApproximation/unittests/FunctionArgumentUnitTest.hpp (added) * src/FunctionApproximation/unittests/Makefile.am (added) * src/unittests/Makefile.am (modified) Argument_t now has two Comparators on indices or distance. - added ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [d03292] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionModel.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) * src/Potentials/Specifics/PairPotential_Morse.hpp (modified) Implemented box constraints for FunctionModel, using a feature of ... Wed, 19 Dec 2012 15:26:11 GMT Frederik Heber [eb1efe] * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.cpp (modified) * src/Potentials/Specifics/unittests/ManyBodyPotential_TersoffUnitTest.hpp (modified) Extended LevMartester to fit a Tersoff potential to the first order ... Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber [9e903b] * src/FunctionApproximation/FunctionArgument.cpp (added) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/FunctionApproximation/Makefile.am (modified) Added operator<<() to FunctionArgument. Wed, 19 Dec 2012 15:25:32 GMT Frederik Heber [371c8b] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) Added FunctionApproximation::checkParameterDerivatives(). - ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [63b9f7] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) REFACTOR: Split off prepareModel() and prepareOutput() from ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [76e63d] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) Extended FunctionApproximation::operator() to receive JacobianMode ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [5b5724] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/FunctionApproximation/FunctionApproximation.hpp (modified) * src/FunctionApproximation/FunctionArgument.hpp (modified) * src/LevMartester.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.cpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) FunctionApproximation now uses levmar_der, i.e. additionally the ... Wed, 19 Dec 2012 15:25:31 GMT Frederik Heber [3ccea3] * src/FunctionApproximation/FunctionModel.hpp (modified) * src/Potentials/EmpiricalPotential.hpp (modified) * src/Potentials/Specifics/ManyBodyPotential_Tersoff.hpp (modified) * src/Potentials/Specifics/PairPotential_Harmonic.hpp (modified) EmpiricalPotential and FunctionModel are now inherited virtually, ... Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [c62f96] * src/FunctionApproximation/FunctionApproximation.cpp (modified) * src/LevMartester.cpp (modified) * src/Makefile.am (modified) LevMartester uses now FunctionApproximation. Wed, 19 Dec 2012 15:25:30 GMT Frederik Heber [66cfc7] * src/FunctionApproximation/FunctionApproximation.cpp (added) * src/FunctionApproximation/FunctionApproximation.hpp (added) * src/FunctionApproximation/FunctionArgument.hpp (added) * src/FunctionApproximation/FunctionModel.hpp (added) * src/FunctionApproximation/Makefile.am (added) * src/Makefile.am (modified) Added new class FunctionApproximation that encapsulates the LevMar ...